DendroPy

It provides classes and functions for working with phylogenetic data such as trees and character matrices.

It also supports reading and writing of the data in a range of standard phylogenetic data formats, such as NEXUS, NeXML, Phylip, NEWICK, FASTA, etc..

In addition, scripts for performing some useful phylogenetic computations are distributed as part of the library, such as SumTrees, which summarizes the support for splits or clades given by a posterior sample of phylogenetic trees.

There are extended documentation and tutorial files in the download package.

What is new in this release:

• New infrastructure for metadata annotations: AnnotationSet and Annotation.
• Full support of NeXML 0.9 metadata parsing and writing.
• get_from_url() and read_from_url() methods now allow for reading of phylogenetic data from URL's.
• Added GBIF interoperability module ("dendropy.interop.gbif").

What is new in version 3.12.2:

• New infrastructure for metadata annotations: AnnotationSet and Annotation.
• Full support of NeXML 0.9 metadata parsing and writing.
• get_from_url() and read_from_url() methods now allow for reading of phylogenetic data from URL's.
• Added GBIF interoperability module ("dendropy.interop.gbif").

What is new in version 3.11.0:

• New application script for concatenation of branch labels from across multiple input trees: sumlabels.py.
• New interoperability class dendropy.interop.seqgen.SeqGen: wrapper for Seq-Gen integrated into library.
• New interoperability function dendropy.interop.muscle.muscle_align(): wrapper for MUSCLE alignment.
• New interoperability class dendropy.interop.raxml.RaxmlRunner: wrapper for RAxML.
• prune_taxa() method added to CharacterMatrix.
• Math modules moved to their own subpackage: dendropy.mathlib.
• New module for matrix and vector computations: dendropy.mathlib.linearalg.
• New module for statistical distance calculation: dendropy.mathlib.distance.
• Family of Mahalanobis distance calculation functions in dendropy.mathlib.distance: squared_mahalanobis, squared_mahalanobis_1d, mahalanobis, mahalanobis_1d.

What is new in version 3.9.0:

• New Features:
• Phylogenetic independent contrasts (PIC) analysis can now be carried out using the dendropy.continuous.PhylogeneticIndependentContrasts class.
• Simplified contained coalescent (gene tree in species tree) simulation.
• Changes:
• Keyword arguments to as_string(), write_to_path(), write_to_file, etc. methods have been tweaked to become more consistent for NEXUS and Newick formats. Previous keywords are still supported, but will be deprecated. The new set of keyword arguments supported can be seen in the :ref:NEXUS and Newick writing customization <Customizing_Writing_NEXUS_and_Newick> section.
• NEXUS and Newick formats now default to case-insensitive taxon labels; specify case_insensitive_taxon_labels=False for case-sensitivity.
• Bug Fixes:
• Reading interleaved character matrices no longer results in the following block being skipped (NEXUS).
• Caught OverflowError when calculating summary statistics.

What is new in version 3.8.0:

• Tree objects can now be rerooted at midpoint (see Tree.reroot_at_midpoint()).
• Annotations (i.e., attributes of Tree, Node or Edge objects that have had "annotate()" called on them) can now be written as metadata comments ("[&field=value]") when writing NEXUS/NEWICK format if the keyword argument annotations_as_comments is used.
• When reading in NEXUS/NEWICK format trees, specifying extract_comment_metadata=True will result in metadata comments being pulled into dictionary, with keys being fieldnames and values being the field values.
• When reading NEXUS format data, SETS blocks will be processed, and character sets parsed into the relevant CharacterDataMatrix.
• Character sets (as, for example, parsed out of NEXUS SETS blocks: see above) can be exported as new CharacterDataMatrix objects, and be saved/manipulated/etc. independentally.
• When writing in NEXUS or NEWICK formats, the write_item_comments keyword argument (True or False) can control whether extended comments associated with nodes on trees will be written or not.
• TopologyCounter class added to dendropy.treesum: allows for tracking of topology frequencies.
• treesplits.tree_from_splits() allows constructing of (topology-only) trees from a set of splits.
• Most functionality that used to be ‘dendropy.treemanip' has now been migrated as native methods of the dendropy.Tree class. ‘dendropy.treemanip' will be deprecated.
• Trees can now be pruned based on a list of taxa labels to remove or keep (previously, the methods would only accept lists of Taxon objects).

What is new in version 3.7.1:

• New Features:
• Implementation of the ‘General Sampling Approach' (Hartman et al. 2010: Sampling Trees from Evolutionary Models; Syst. Biol. 49, 465-476) method of simulating trees from the birth-death model.
• Changes:
• Correct/consistent names for some probability functions.
• Bug Fixes:
• Bug in confirming overwriting of output file when using SumTrees ‘-e'/'-split-edges' option.
• Ancient and grizzled semi-fossilized reference to ‘taxa_block' corrected to ‘taxon_set'.

What is new in version 3.7.0:

• Migrated to BSD-style license.

What is new in version 3.6.1:

• SumTrees now works (in serial mode) under older Python versions (i.e. < 2.6).
• Fixes for compatibility with Python 2.4.x.

What is new in version 3.5.0:

• Added ladderize() method, to order nodes in ascending (default) or descending (ladderize(right=True)) order.
• Added "beast-summary-tree" schema specification to process BEAST annotated consensus trees.
• Added new module for interacting with NCBI databases: dendropy.interop.ncbi.

What is new in version 3.4.:

• Bundled ez_setup.py updated to latest version.

Requirements:

• Python 2.4 to 3.0